[chimerax-users] [EXTERNAL] Measuring surface area of a colored portion of the map

[Elaine Meng]

Hi,
Although both the Segment Map and the Measure Color and Blobs tools have been added to ChimeraX (Segment Map added July 2019, Measure and Color Blobs in May 2019), that approach may not be what you had in mind, because it would make separate segmentation surfaces. Also it may be hard to get the areas of interest to segment separately... and if you were going to make two separate surfaces anyway, probably the split by color zone approach you already mentioned would be much easier.

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/measureblobs.html>

The ChimeraX change log shows the approximate dates that features were added:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>

If I understand Yaikhomba's question correctly, he just wants to measure the surface areas of different colors in a single isosurface.  However, I don't know of a way, or at least I haven't thought of how to do it, in either Chimera or ChimeraX.  (Other than writing some kind of python script, which I don't know how to do either.)  If I think of a way, will let you know.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On May 18, 2021, at 2:06 PM, Reza Khayat <rkhayat at ccny.cuny.edu> wrote:
> 
> ​Hi,
> 
> Not sure if this is possible in ChimeraX yet but can do this in Chimera. Use map segmentation to separate green from grey. Then use surface measure tool (Mesure and color Blobs) to measure the surface area. 
> 
> Best wishes,
> Reza
> 
> Reza Khayat, PhD
> Associate Professor 
> City College of New York
> Department of Chemistry and Biochemistry
> New York, NY 10031
> From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Y. Mutum <ym337 at cam.ac.uk>
> Sent: Tuesday, May 18, 2021 4:47 PM
> To: chimerax-users at cgl.ucsf.edu
> Subject: [EXTERNAL] [chimerax-users] Measuring surface area of a colored portion of the map
>  
> Hi
> 
> This problem relates to surface area of a low-resolution EM map using ChimeraX
> 
> I have opened the following map and the corresponding model using the following commands in ChimeraX. 
> 
> >>> open 4uq8; open 2676 from emdb
> >>> color #1 green; color zone #2 near #1 dist 4
> 
> As many parts of the map are unmodelled, I am interested 'how much of the map is unmodelled' in terms of surface area.  This is mainly because the model is not accurate and I am trying to only use the raw-data (map) to estimate the surface area and avoid using the model.
> 
> Is there a way to figure out how much of the map is unmodelled in terms of surface area? In this case, count the number of 'outer pixels of a map' that are colored green or gray, at a given map contour? 
> 
> Could you please help with a way to measure this without using the 'volume splitbyzone' command?
> 
> Thanks
> Yaikhomba
> 
> <image.png>
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